With a growing interest in personalized medicine, functional neuroimaging research has recently shifted focus from the evaluation of group-level summaries to associating individual differences in brain function with behaviors. However, this new focus brings forth challenges related to accurately measuring the sources of individual variation in functional signals. In this perspective, we highlight the impact of within-individual variations and discuss the concept of measurement reliability as a critical tool for accounting for within- and between-individual variations when measuring individual differences in brain function.